Starting phenix.real_space_refine
on Thu Jul  2 17:13:22 2026 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/9nzq_49956/07_2026/9nzq_49956.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9nzq_49956/07_2026/9nzq_49956.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.67
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9nzq_49956/07_2026/9nzq_49956.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9nzq_49956/07_2026/9nzq_49956.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9nzq_49956/07_2026/9nzq_49956.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9nzq_49956/07_2026/9nzq_49956.cif"
  }
  resolution = 3.67
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.013
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P     152      5.49       5
     S      40      5.16       5
     C    5258      2.51       5
     N    1677      2.21       5
     O    2130      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 9258
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3386
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 423, 3386
          Classifications: {'peptide': 423}
          Link IDs: {'PTRANS': 11, 'TRANS': 411}
    Chain: "B"
      Number of atoms: 2629
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 327, 2629
          Classifications: {'peptide': 327}
          Link IDs: {'PTRANS': 9, 'TRANS': 317}
          Chain breaks: 5
    Chain: "C"
      Number of atoms: 331
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 331
          Classifications: {'DNA': 16}
          Link IDs: {'rna3p': 15}
    Chain: "D"
      Number of atoms: 163
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 163
          Classifications: {'DNA': 8}
          Link IDs: {'rna3p': 7}
    Chain: "E"
      Number of atoms: 2748
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 2748
          Classifications: {'RNA': 128}
          Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 10, 'rna3p_pur': 60, 'rna3p_pyr': 44}
          Link IDs: {'rna2p': 24, 'rna3p': 103}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   3013  SG  CYS A 377      18.032  83.772  72.324  1.00 55.33           S
  ATOM   3036  SG  CYS A 380      14.978  86.360  70.972  1.00 65.53           S
  ATOM   3157  SG  CYS A 396      18.685  87.212  70.940  1.00 62.24           S
  ATOM   3179  SG  CYS A 399      16.933  86.920  74.005  1.00 58.21           S

  Time building chain proxies: 2.39, per 1000 atoms: 0.26
  Number of scatterers: 9258
  At special positions: 0
  Unit cell: (94, 111.86, 121.26, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      1     29.99
     S      40     16.00
     P     152     15.00
     O    2130      8.00
     N    1677      7.00
     C    5258      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.83
  Conformation dependent library (CDL) restraints added in 207.8 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 501 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 399 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 396 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 380 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 377 "
      Number of angles added : 6


  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1406

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 7 sheets defined
      50.9% alpha, 7.2% beta
      43 base pairs and 83 stacking pairs defined.
    Time for finding SS restraints: 1.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 62
    Processing helix  chain 'A' and resid 67 through 72
      removed outlier: 3.801A  pdb=" N   GLU A  71 " --> pdb=" O   ASP A  67 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 89
      removed outlier: 3.747A  pdb=" N   HIS A  80 " --> pdb=" O   ARG A  76 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   GLY A  87 " --> pdb=" O   ASN A  83 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   GLN A  88 " --> pdb=" O   CYS A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 93 through 111
      removed outlier: 3.598A  pdb=" N   LYS A 107 " --> pdb=" O   LYS A 103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 117
    Processing helix  chain 'A' and resid 134 through 136
      No H-bonds generated for 'chain 'A' and resid 134 through 136'
    Processing helix  chain 'A' and resid 156 through 162
    Processing helix  chain 'A' and resid 178 through 188
      removed outlier: 4.155A  pdb=" N   PHE A 182 " --> pdb=" O   GLN A 178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 250 through 271
      removed outlier: 3.631A  pdb=" N   ALA A 257 " --> pdb=" O   ILE A 253 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ALA A 271 " --> pdb=" O   MET A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 319
    Processing helix  chain 'A' and resid 347 through 362
    Processing helix  chain 'A' and resid 384 through 388
      removed outlier: 3.596A  pdb=" N   ARG A 388 " --> pdb=" O   LYS A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 415
    Processing helix  chain 'A' and resid 417 through 427
      removed outlier: 3.840A  pdb=" N   ILE A 421 " --> pdb=" O   ASN A 417 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 22 through 54
    Processing helix  chain 'B' and resid 77 through 89
    Processing helix  chain 'B' and resid 93 through 111
    Processing helix  chain 'B' and resid 111 through 117
    Processing helix  chain 'B' and resid 156 through 162
    Processing helix  chain 'B' and resid 178 through 188
      removed outlier: 3.883A  pdb=" N   PHE B 182 " --> pdb=" O   GLN B 178 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 250 through 274
    Processing helix  chain 'B' and resid 294 through 319
    Processing helix  chain 'B' and resid 346 through 361
      removed outlier: 3.822A  pdb=" N   LEU B 350 " --> pdb=" O   THR B 346 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 406 through 415
      removed outlier: 3.677A  pdb=" N   ILE B 415 " --> pdb=" O   GLN B 411 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 417 through 427
    Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 13
      removed outlier: 3.504A  pdb=" N   PHE A 205 " --> pdb=" O   TYR A 199 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   LEU A 197 " --> pdb=" O   PHE A 207 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   VAL A 198 " --> pdb=" O   LEU A 131 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   LEU A 131 " --> pdb=" O   VAL A 198 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 138 through 141
      removed outlier: 3.691A  pdb=" N   ILE A 148 " --> pdb=" O   LEU A 173 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 235 through 237
      removed outlier: 3.598A  pdb=" N   LEU A 235 " --> pdb=" O   ILE A 248 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 133 through 134
    Processing sheet with id=AA5, first strand: chain 'B' and resid 138 through 140
    Processing sheet with id=AA6, first strand: chain 'B' and resid 226 through 230
      removed outlier: 5.115A  pdb=" N   GLY B 230 " --> pdb=" O   ALA B 234 " (cutoff:3.500A)
      removed outlier: 4.863A  pdb=" N   ALA B 234 " --> pdb=" O   GLY B 230 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 324 through 327
      removed outlier: 3.670A  pdb=" N   VAL B 366 " --> pdb=" O   ILE B 324 " (cutoff:3.500A)

    305 hydrogen bonds defined for protein.
    897 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      110 hydrogen bonds
      212 hydrogen bond angles
      0 basepair planarities
      43 basepair parallelities
      83 stacking parallelities
  Total time for adding SS restraints: 1.66

  Time building geometry restraints manager: 1.03 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.20 -     1.32: 1366
        1.32 -     1.45: 3457
        1.45 -     1.57: 4577
        1.57 -     1.70: 301
        1.70 -     1.82: 61
  Bond restraints: 9762
  Sorted by residual:
  bond pdb=" N9    A E  40 "
       pdb=" C4    A E  40 "
    ideal  model  delta    sigma   weight residual
    1.374  1.396 -0.022 6.00e-03 2.78e+04 1.32e+01
  bond pdb=" N9    A E  69 "
       pdb=" C4    A E  69 "
    ideal  model  delta    sigma   weight residual
    1.374  1.395 -0.021 6.00e-03 2.78e+04 1.22e+01
  bond pdb=" N9    A E  99 "
       pdb=" C4    A E  99 "
    ideal  model  delta    sigma   weight residual
    1.374  1.395 -0.021 6.00e-03 2.78e+04 1.20e+01
  bond pdb=" N9    A E  65 "
       pdb=" C4    A E  65 "
    ideal  model  delta    sigma   weight residual
    1.374  1.392 -0.018 6.00e-03 2.78e+04 9.17e+00
  bond pdb=" N9    A E  83 "
       pdb=" C4    A E  83 "
    ideal  model  delta    sigma   weight residual
    1.374  1.391 -0.017 6.00e-03 2.78e+04 8.43e+00
  ... (remaining 9757 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.56: 13229
        2.56 -     5.11: 515
        5.11 -     7.67: 105
        7.67 -    10.22: 24
       10.22 -    12.78: 12
  Bond angle restraints: 13885
  Sorted by residual:
  angle pdb=" N1    C E  66 "
        pdb=" C2    C E  66 "
        pdb=" O2    C E  66 "
      ideal   model   delta    sigma   weight residual
     118.90  124.36   -5.46 6.00e-01 2.78e+00 8.27e+01
  angle pdb=" N   MET B  26 "
        pdb=" CA  MET B  26 "
        pdb=" CB  MET B  26 "
      ideal   model   delta    sigma   weight residual
     110.01  120.25  -10.24 1.45e+00 4.76e-01 4.99e+01
  angle pdb=" C1'   C E  66 "
        pdb=" N1    C E  66 "
        pdb=" C2    C E  66 "
      ideal   model   delta    sigma   weight residual
     118.80  126.46   -7.66 1.10e+00 8.26e-01 4.85e+01
  angle pdb=" O2    C E  66 "
        pdb=" C2    C E  66 "
        pdb=" N3    C E  66 "
      ideal   model   delta    sigma   weight residual
     121.90  117.30    4.60 7.00e-01 2.04e+00 4.32e+01
  angle pdb=" CA  MET B 120 "
        pdb=" CB  MET B 120 "
        pdb=" CG  MET B 120 "
      ideal   model   delta    sigma   weight residual
     114.10  126.88  -12.78 2.00e+00 2.50e-01 4.08e+01
  ... (remaining 13880 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.77: 5269
       32.77 -    65.54: 643
       65.54 -    98.32: 54
       98.32 -   131.09: 5
      131.09 -   163.86: 8
  Dihedral angle restraints: 5979
    sinusoidal: 3796
      harmonic: 2183
  Sorted by residual:
  dihedral pdb=" C5'   U E 140 "
           pdb=" C4'   U E 140 "
           pdb=" C3'   U E 140 "
           pdb=" O3'   U E 140 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.00   80.88   66.12     1      8.00e+00 1.56e-02 8.93e+01
  dihedral pdb=" C4'   U E 140 "
           pdb=" C3'   U E 140 "
           pdb=" C2'   U E 140 "
           pdb=" C1'   U E 140 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -35.00   28.90  -63.90     1      8.00e+00 1.56e-02 8.40e+01
  dihedral pdb=" O4'   C E  19 "
           pdb=" C1'   C E  19 "
           pdb=" N1    C E  19 "
           pdb=" C2    C E  19 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   45.28  154.72     1      1.50e+01 4.44e-03 8.12e+01
  ... (remaining 5976 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.073: 1349
       0.073 -    0.147: 228
       0.147 -    0.220: 31
       0.220 -    0.293: 8
       0.293 -    0.366: 3
  Chirality restraints: 1619
  Sorted by residual:
  chirality pdb=" CA  MET B  26 "
            pdb=" N   MET B  26 "
            pdb=" C   MET B  26 "
            pdb=" CB  MET B  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.35e+00
  chirality pdb=" CB  ILE B 324 "
            pdb=" CA  ILE B 324 "
            pdb=" CG1 ILE B 324 "
            pdb=" CG2 ILE B 324 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.30    0.35 2.00e-01 2.50e+01 2.99e+00
  chirality pdb=" C3'   U E 140 "
            pdb=" C4'   U E 140 "
            pdb=" O3'   U E 140 "
            pdb=" C2'   U E 140 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.42   -0.32 2.00e-01 2.50e+01 2.62e+00
  ... (remaining 1616 not shown)

  Planarity restraints: 1207
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G E 127 "    0.031 2.00e-02 2.50e+03   2.76e-02 2.29e+01
        pdb=" N9    G E 127 "   -0.031 2.00e-02 2.50e+03
        pdb=" C8    G E 127 "   -0.000 2.00e-02 2.50e+03
        pdb=" N7    G E 127 "    0.004 2.00e-02 2.50e+03
        pdb=" C5    G E 127 "    0.001 2.00e-02 2.50e+03
        pdb=" C6    G E 127 "   -0.018 2.00e-02 2.50e+03
        pdb=" O6    G E 127 "    0.021 2.00e-02 2.50e+03
        pdb=" N1    G E 127 "    0.016 2.00e-02 2.50e+03
        pdb=" C2    G E 127 "   -0.069 2.00e-02 2.50e+03
        pdb=" N2    G E 127 "    0.037 2.00e-02 2.50e+03
        pdb=" N3    G E 127 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4    G E 127 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 407 "    0.025 2.00e-02 2.50e+03   2.77e-02 1.34e+01
        pdb=" CG  PHE A 407 "   -0.064 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 407 "    0.012 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 407 "    0.019 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 407 "    0.008 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 407 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 407 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 240 "    0.018 2.00e-02 2.50e+03   2.66e-02 1.23e+01
        pdb=" CG  PHE B 240 "   -0.060 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 240 "    0.023 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 240 "    0.020 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 240 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 240 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 240 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 1204 not shown)

  Histogram of nonbonded interaction distances:
        2.43 -     2.93: 3559
        2.93 -     3.42: 9246
        3.42 -     3.91: 17099
        3.91 -     4.41: 18315
        4.41 -     4.90: 26932
  Nonbonded interactions: 75151
  Sorted by model distance:
  nonbonded pdb=" N1    A E  34 "
            pdb=" O6    G E  64 "
     model   vdw
     2.434 2.496
  nonbonded pdb=" O4'   C E  70 "
            pdb=" C6    C E  70 "
     model   vdw
     2.481 2.672
  nonbonded pdb=" O5'   G E 116 "
            pdb=" O4'   G E 116 "
     model   vdw
     2.519 2.432
  nonbonded pdb=" O4'   C E  66 "
            pdb=" C6    C E  66 "
     model   vdw
     2.526 2.672
  nonbonded pdb=" N   ARG B 201 "
            pdb=" O   ARG B 201 "
     model   vdw
     2.527 2.496
  ... (remaining 75146 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.180
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.140
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6961
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.098   9766  Z= 0.391
  Angle     :  1.243  18.404  13891  Z= 0.837
  Chirality :  0.058   0.366   1619
  Planarity :  0.010   0.100   1207
  Dihedral  : 24.090 163.859   4573
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 28.68 %
    Favored  : 70.23 %
  Cbeta Deviations :  0.14 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.43 (0.30), residues: 736
  helix:  0.49 (0.27), residues: 347
  sheet: -2.25 (0.48), residues: 117
  loop : -2.20 (0.34), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.023   0.004   ARG B  76 
 TYR   0.034   0.003   TYR A 125 
 PHE   0.064   0.005   PHE A 407 
 TRP   0.033   0.003   TRP A  51 
 HIS   0.021   0.002   HIS B  80 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00631 /  0.39 ( 9762)
  covalent geometry    : angle       1.22868 /  0.84 (13885)
  hydrogen bonds       : bond        0.14312 /  9.50 (  415)
  hydrogen bonds       : angle       5.62870 /  4.04 ( 1109)
  metal coordination   : bond        0.01799 /  0.89 (    4)
  metal coordination   : angle       9.04006 /  3.85 (    6)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 75
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  128 ASN cc_start: 0.7493 (t0) cc_final: 0.6939 (t0)
  outliers start: 7
  outliers final: 3
  residues processed: 81
  average time/residue: 0.1163
  time to fit residues: 12.5595
Evaluate side-chains
  59 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 56
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 ILE
Chi-restraints excluded: chain A residue  338 PHE
Chi-restraints excluded: chain A residue  372 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:   20.0000
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    4.9990
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:   10.9990
   overall best weight:    3.3990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  46 GLN
** A  59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 319 ASN
A 320 GLN
A 391 GLN
A 411 GLN
A 412 ASN
B  25 ASN
B  80 HIS
B 184 ASN
B 217 HIS
B 273 HIS
** B 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.071600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.054147 restraints weight = 50637.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.055847 restraints weight = 24390.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.056889 restraints weight = 16095.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.057470 restraints weight = 12792.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.057745 restraints weight = 11326.476|
|-----------------------------------------------------------------------------|
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8114
moved from start:          0.1704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.088   9766  Z= 0.267
  Angle     :  0.771  13.361  13891  Z= 0.427
  Chirality :  0.042   0.278   1619
  Planarity :  0.005   0.056   1207
  Dihedral  : 24.901 163.386   3083
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 15.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  5.27 %
    Allowed  : 24.81 %
    Favored  : 69.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.50 (0.31), residues: 736
  helix:  1.40 (0.27), residues: 354
  sheet: -1.86 (0.48), residues: 124
  loop : -1.98 (0.36), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 301 
 TYR   0.019   0.002   TYR A 348 
 PHE   0.024   0.003   PHE B 300 
 TRP   0.021   0.002   TRP A  51 
 HIS   0.007   0.001   HIS B  80 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00553 /  0.27 ( 9762)
  covalent geometry    : angle       0.76066 /  0.43 (13885)
  hydrogen bonds       : bond        0.07032 /  4.64 (  415)
  hydrogen bonds       : angle       4.63488 /  3.37 ( 1109)
  metal coordination   : bond        0.02001 /  0.94 (    4)
  metal coordination   : angle       6.23061 /  2.58 (    6)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 59
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8606 (mp)
REVERT: A  121 SER cc_start: 0.8865 (OUTLIER) cc_final: 0.8341 (p)
REVERT: A  212 PHE cc_start: 0.6930 (OUTLIER) cc_final: 0.6704 (m-10)
REVERT: A  267 MET cc_start: 0.8976 (OUTLIER) cc_final: 0.8745 (mmm)
REVERT: A  314 ASP cc_start: 0.8461 (m-30) cc_final: 0.8249 (m-30)
REVERT: A  371 ARG cc_start: 0.8288 (tpt90) cc_final: 0.8024 (tpt90)
REVERT: A  410 SER cc_start: 0.9042 (OUTLIER) cc_final: 0.8427 (t)
REVERT: B   16 TYR cc_start: 0.7765 (OUTLIER) cc_final: 0.6860 (p90)
REVERT: B   26 MET cc_start: 0.8726 (mpp) cc_final: 0.8358 (mpp)
REVERT: B  306 HIS cc_start: 0.9565 (OUTLIER) cc_final: 0.9269 (t-90)
REVERT: B  372 HIS cc_start: 0.7292 (t70) cc_final: 0.7065 (t70)
  outliers start: 34
  outliers final: 11
  residues processed: 89
  average time/residue: 0.0869
  time to fit residues: 11.0567
Evaluate side-chains
  74 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 56
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 LEU
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue  121 SER
Chi-restraints excluded: chain A residue  124 SER
Chi-restraints excluded: chain A residue  174 HIS
Chi-restraints excluded: chain A residue  212 PHE
Chi-restraints excluded: chain A residue  267 MET
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  338 PHE
Chi-restraints excluded: chain A residue  410 SER
Chi-restraints excluded: chain B residue   16 TYR
Chi-restraints excluded: chain B residue   40 ILE
Chi-restraints excluded: chain B residue  195 CYS
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  306 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 11 optimal weight:    0.5980
   chunk 12 optimal weight:    3.9990
   chunk 73 optimal weight:   10.0000
   chunk 24 optimal weight:    2.9990
   chunk 4 optimal weight:    0.8980
   chunk 38 optimal weight:   10.0000
   chunk 55 optimal weight:   20.0000
   chunk 32 optimal weight:    0.0070
   chunk 10 optimal weight:    1.9990
   chunk 65 optimal weight:   20.0000
   chunk 77 optimal weight:   10.0000
   overall best weight:    1.3002

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  80 HIS
** B 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.072769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.055600 restraints weight = 50707.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.057353 restraints weight = 24237.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.058421 restraints weight = 15939.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.059050 restraints weight = 12658.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.059316 restraints weight = 11172.043|
|-----------------------------------------------------------------------------|
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
moved from start:          0.1883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9766  Z= 0.152
  Angle     :  0.638  12.848  13891  Z= 0.355
  Chirality :  0.039   0.278   1619
  Planarity :  0.004   0.050   1207
  Dihedral  : 24.801 167.467   3079
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 11.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 26.82 %
    Favored  : 69.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.05 (0.31), residues: 736
  helix:  1.84 (0.26), residues: 355
  sheet: -1.40 (0.47), residues: 125
  loop : -1.84 (0.37), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 179 
 TYR   0.015   0.001   TYR A 125 
 PHE   0.011   0.002   PHE B 169 
 TRP   0.014   0.001   TRP A  51 
 HIS   0.003   0.001   HIS B 306 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00301 /  0.15 ( 9762)
  covalent geometry    : angle       0.62438 /  0.35 (13885)
  hydrogen bonds       : bond        0.06071 /  3.93 (  415)
  hydrogen bonds       : angle       4.11462 /  2.97 ( 1109)
  metal coordination   : bond        0.01081 /  0.52 (    4)
  metal coordination   : angle       6.22570 /  2.61 (    6)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 56
  time to evaluate  : 0.170 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8585 (mp)
REVERT: A  145 ARG cc_start: 0.8462 (tpt90) cc_final: 0.8237 (tpt-90)
REVERT: A  210 TYR cc_start: 0.8294 (OUTLIER) cc_final: 0.7931 (m-80)
REVERT: A  267 MET cc_start: 0.8986 (tpp) cc_final: 0.8679 (mmm)
REVERT: A  314 ASP cc_start: 0.8398 (m-30) cc_final: 0.8167 (m-30)
REVERT: B   16 TYR cc_start: 0.7810 (OUTLIER) cc_final: 0.6874 (p90)
REVERT: B   26 MET cc_start: 0.8697 (mpp) cc_final: 0.7970 (mpp)
REVERT: B  306 HIS cc_start: 0.9511 (OUTLIER) cc_final: 0.9238 (t-90)
REVERT: B  372 HIS cc_start: 0.7242 (t70) cc_final: 0.7008 (t70)
  outliers start: 26
  outliers final: 12
  residues processed: 79
  average time/residue: 0.0964
  time to fit residues: 10.6596
Evaluate side-chains
  69 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 53
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 LEU
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue  124 SER
Chi-restraints excluded: chain A residue  135 LYS
Chi-restraints excluded: chain A residue  210 TYR
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  338 PHE
Chi-restraints excluded: chain A residue  372 HIS
Chi-restraints excluded: chain B residue   16 TYR
Chi-restraints excluded: chain B residue   40 ILE
Chi-restraints excluded: chain B residue  195 CYS
Chi-restraints excluded: chain B residue  201 ARG
Chi-restraints excluded: chain B residue  306 HIS
Chi-restraints excluded: chain B residue  407 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   chunk 59 optimal weight:    7.9990
   chunk 60 optimal weight:    8.9990
   chunk 68 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9980
   chunk 82 optimal weight:   20.0000
   chunk 36 optimal weight:    6.9990
   chunk 8 optimal weight:    6.9990
   chunk 84 optimal weight:   10.0000
   chunk 7 optimal weight:    3.9990
   overall best weight:    1.9386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 412 ASN
** B  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  80 HIS
B 372 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.071409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.054014 restraints weight = 51388.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.055735 restraints weight = 24620.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.056805 restraints weight = 16221.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.057309 restraints weight = 12906.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.057722 restraints weight = 11566.527|
|-----------------------------------------------------------------------------|
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8114
moved from start:          0.2259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   9766  Z= 0.178
  Angle     :  0.629  13.038  13891  Z= 0.347
  Chirality :  0.038   0.264   1619
  Planarity :  0.005   0.049   1207
  Dihedral  : 24.690 168.223   3079
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 13.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  5.58 %
    Allowed  : 25.43 %
    Favored  : 68.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.11 (0.31), residues: 736
  helix:  1.86 (0.26), residues: 355
  sheet: -1.24 (0.47), residues: 125
  loop : -1.84 (0.38), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 201 
 TYR   0.013   0.001   TYR A 348 
 PHE   0.016   0.002   PHE A 394 
 TRP   0.035   0.002   TRP A 345 
 HIS   0.006   0.001   HIS B  80 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00362 /  0.18 ( 9762)
  covalent geometry    : angle       0.61427 /  0.35 (13885)
  hydrogen bonds       : bond        0.05749 /  3.73 (  415)
  hydrogen bonds       : angle       3.99813 /  2.89 ( 1109)
  metal coordination   : bond        0.01090 /  0.51 (    4)
  metal coordination   : angle       6.55572 /  2.82 (    6)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 54
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8547 (mp)
REVERT: A  210 TYR cc_start: 0.8061 (OUTLIER) cc_final: 0.7704 (m-80)
REVERT: A  267 MET cc_start: 0.8975 (tpp) cc_final: 0.8652 (mmm)
REVERT: A  314 ASP cc_start: 0.8449 (m-30) cc_final: 0.8208 (m-30)
REVERT: B   16 TYR cc_start: 0.7939 (OUTLIER) cc_final: 0.6838 (p90)
REVERT: B   26 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.8032 (mpp)
REVERT: B  206 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7827 (tp)
REVERT: B  306 HIS cc_start: 0.9539 (OUTLIER) cc_final: 0.9271 (t-90)
REVERT: B  372 HIS cc_start: 0.7327 (t-90) cc_final: 0.7094 (t70)
  outliers start: 36
  outliers final: 14
  residues processed: 87
  average time/residue: 0.0787
  time to fit residues: 10.0928
Evaluate side-chains
  74 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 54
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 LEU
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue  124 SER
Chi-restraints excluded: chain A residue  135 LYS
Chi-restraints excluded: chain A residue  210 TYR
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  338 PHE
Chi-restraints excluded: chain A residue  411 GLN
Chi-restraints excluded: chain B residue   16 TYR
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   26 MET
Chi-restraints excluded: chain B residue   40 ILE
Chi-restraints excluded: chain B residue  195 CYS
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  306 HIS
Chi-restraints excluded: chain B residue  407 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 6 optimal weight:    0.0000
   chunk 0 optimal weight:    4.9990
   chunk 85 optimal weight:   10.9990
   chunk 71 optimal weight:    8.9990
   chunk 41 optimal weight:    7.9990
   chunk 7 optimal weight:    4.9990
   chunk 32 optimal weight:    5.9990
   chunk 13 optimal weight:    2.9990
   chunk 70 optimal weight:    6.9990
   chunk 16 optimal weight:    1.9990
   chunk 25 optimal weight:    5.9990
   overall best weight:    2.9992

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 184 ASN
A 382 HIS
B  80 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.070080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.052370 restraints weight = 52880.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.054104 restraints weight = 25303.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.055116 restraints weight = 16795.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.055764 restraints weight = 13534.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.056019 restraints weight = 11957.879|
|-----------------------------------------------------------------------------|
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.2703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.096   9766  Z= 0.232
  Angle     :  0.656  13.757  13891  Z= 0.363
  Chirality :  0.040   0.333   1619
  Planarity :  0.005   0.050   1207
  Dihedral  : 24.682 169.784   3079
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 14.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  5.43 %
    Allowed  : 25.89 %
    Favored  : 68.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.00 (0.31), residues: 736
  helix:  1.68 (0.26), residues: 359
  sheet: -1.22 (0.47), residues: 128
  loop : -1.83 (0.39), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  38 
 TYR   0.015   0.002   TYR A 348 
 PHE   0.012   0.002   PHE A 212 
 TRP   0.011   0.002   TRP A  51 
 HIS   0.005   0.001   HIS A 273 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00480 /  0.23 ( 9762)
  covalent geometry    : angle       0.63878 /  0.36 (13885)
  hydrogen bonds       : bond        0.05996 /  3.94 (  415)
  hydrogen bonds       : angle       4.07667 /  2.97 ( 1109)
  metal coordination   : bond        0.01229 /  0.55 (    4)
  metal coordination   : angle       7.19463 /  3.11 (    6)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 55
  time to evaluate  : 0.200 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8587 (mp)
REVERT: A  184 ASN cc_start: 0.8704 (m-40) cc_final: 0.8423 (m-40)
REVERT: A  186 MET cc_start: 0.8297 (mtm) cc_final: 0.8041 (mtm)
REVERT: A  210 TYR cc_start: 0.8323 (OUTLIER) cc_final: 0.8092 (m-80)
REVERT: A  267 MET cc_start: 0.8968 (tpp) cc_final: 0.8612 (mmm)
REVERT: A  372 HIS cc_start: 0.8789 (OUTLIER) cc_final: 0.8568 (t-90)
REVERT: A  389 THR cc_start: 0.8747 (OUTLIER) cc_final: 0.8509 (p)
REVERT: B   16 TYR cc_start: 0.8000 (OUTLIER) cc_final: 0.6979 (p90)
REVERT: B   26 MET cc_start: 0.8830 (OUTLIER) cc_final: 0.8151 (mpp)
REVERT: B  206 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.7975 (tp)
REVERT: B  306 HIS cc_start: 0.9579 (OUTLIER) cc_final: 0.9324 (t-90)
  outliers start: 35
  outliers final: 19
  residues processed: 87
  average time/residue: 0.0753
  time to fit residues: 9.3799
Evaluate side-chains
  78 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 51
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 LEU
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue   81 ILE
Chi-restraints excluded: chain A residue  124 SER
Chi-restraints excluded: chain A residue  135 LYS
Chi-restraints excluded: chain A residue  174 HIS
Chi-restraints excluded: chain A residue  210 TYR
Chi-restraints excluded: chain A residue  243 HIS
Chi-restraints excluded: chain A residue  273 HIS
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  338 PHE
Chi-restraints excluded: chain A residue  372 HIS
Chi-restraints excluded: chain A residue  389 THR
Chi-restraints excluded: chain A residue  411 GLN
Chi-restraints excluded: chain B residue   16 TYR
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   26 MET
Chi-restraints excluded: chain B residue   40 ILE
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  195 CYS
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  306 HIS
Chi-restraints excluded: chain B residue  328 ASP
Chi-restraints excluded: chain B residue  407 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 46 optimal weight:    0.3980
   chunk 20 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9990
   chunk 82 optimal weight:   10.0000
   chunk 54 optimal weight:    0.7980
   chunk 40 optimal weight:    1.9990
   chunk 63 optimal weight:    4.9990
   chunk 78 optimal weight:   20.0000
   chunk 85 optimal weight:   20.0000
   chunk 12 optimal weight:    8.9990
   chunk 86 optimal weight:    7.9990
   overall best weight:    1.0184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  98 ASN
A 184 ASN
B  80 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.071356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.054054 restraints weight = 51430.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.055778 restraints weight = 24788.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.056847 restraints weight = 16450.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.057460 restraints weight = 13117.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.057725 restraints weight = 11615.345|
|-----------------------------------------------------------------------------|
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8119
moved from start:          0.2768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9766  Z= 0.136
  Angle     :  0.611  13.650  13891  Z= 0.332
  Chirality :  0.038   0.425   1619
  Planarity :  0.004   0.049   1207
  Dihedral  : 24.660 171.464   3079
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 12.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 25.89 %
    Favored  : 69.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.18 (0.31), residues: 736
  helix:  1.79 (0.26), residues: 359
  sheet: -0.82 (0.46), residues: 126
  loop : -1.90 (0.39), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  38 
 TYR   0.011   0.001   TYR A 125 
 PHE   0.020   0.001   PHE A 394 
 TRP   0.012   0.001   TRP A 345 
 HIS   0.006   0.001   HIS B  80 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00268 /  0.14 ( 9762)
  covalent geometry    : angle       0.59761 /  0.33 (13885)
  hydrogen bonds       : bond        0.05551 /  3.56 (  415)
  hydrogen bonds       : angle       3.79231 /  2.75 ( 1109)
  metal coordination   : bond        0.01003 /  0.48 (    4)
  metal coordination   : angle       6.05165 /  2.55 (    6)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 54
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7674 (mp)
REVERT: A  210 TYR cc_start: 0.8058 (OUTLIER) cc_final: 0.7757 (m-80)
REVERT: A  267 MET cc_start: 0.8921 (tpp) cc_final: 0.8577 (mmm)
REVERT: A  314 ASP cc_start: 0.8345 (m-30) cc_final: 0.8064 (m-30)
REVERT: A  371 ARG cc_start: 0.8815 (tpm170) cc_final: 0.8434 (mmm160)
REVERT: B   16 TYR cc_start: 0.7976 (OUTLIER) cc_final: 0.7009 (p90)
REVERT: B   26 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8063 (mpp)
REVERT: B  206 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7941 (tp)
REVERT: B  306 HIS cc_start: 0.9506 (OUTLIER) cc_final: 0.9281 (t-90)
  outliers start: 32
  outliers final: 18
  residues processed: 82
  average time/residue: 0.0785
  time to fit residues: 9.4306
Evaluate side-chains
  76 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 52
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue  102 GLN
Chi-restraints excluded: chain A residue  124 SER
Chi-restraints excluded: chain A residue  135 LYS
Chi-restraints excluded: chain A residue  210 TYR
Chi-restraints excluded: chain A residue  273 HIS
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  338 PHE
Chi-restraints excluded: chain A residue  410 SER
Chi-restraints excluded: chain A residue  411 GLN
Chi-restraints excluded: chain B residue   16 TYR
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   26 MET
Chi-restraints excluded: chain B residue   40 ILE
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  195 CYS
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  306 HIS
Chi-restraints excluded: chain B residue  328 ASP
Chi-restraints excluded: chain B residue  407 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 70 optimal weight:    3.9990
   chunk 83 optimal weight:   10.0000
   chunk 13 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9990
   chunk 67 optimal weight:    7.9990
   chunk 7 optimal weight:    5.9990
   chunk 74 optimal weight:   20.0000
   overall best weight:    2.7990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  80 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.069527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.051691 restraints weight = 52951.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.053395 restraints weight = 25664.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.054453 restraints weight = 17236.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.055022 restraints weight = 13811.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.055385 restraints weight = 12348.574|
|-----------------------------------------------------------------------------|
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8193
moved from start:          0.3124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.097   9766  Z= 0.230
  Angle     :  0.658  14.052  13891  Z= 0.360
  Chirality :  0.040   0.343   1619
  Planarity :  0.005   0.048   1207
  Dihedral  : 24.597 167.554   3079
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 16.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 26.98 %
    Favored  : 67.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.14 (0.31), residues: 736
  helix:  1.72 (0.26), residues: 360
  sheet: -1.01 (0.47), residues: 128
  loop : -1.77 (0.40), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  38 
 TYR   0.015   0.002   TYR A 348 
 PHE   0.009   0.001   PHE A  49 
 TRP   0.013   0.002   TRP A  51 
 HIS   0.005   0.001   HIS A 273 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00476 /  0.23 ( 9762)
  covalent geometry    : angle       0.64070 /  0.36 (13885)
  hydrogen bonds       : bond        0.05798 /  3.77 (  415)
  hydrogen bonds       : angle       3.96146 /  2.89 ( 1109)
  metal coordination   : bond        0.01227 /  0.55 (    4)
  metal coordination   : angle       7.22522 /  3.12 (    6)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 52
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8599 (mp)
REVERT: A  267 MET cc_start: 0.8936 (tpp) cc_final: 0.8573 (mmm)
REVERT: A  410 SER cc_start: 0.9392 (OUTLIER) cc_final: 0.8739 (t)
REVERT: B   16 TYR cc_start: 0.7966 (OUTLIER) cc_final: 0.7087 (p90)
REVERT: B   26 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8173 (mpp)
REVERT: B  206 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.7965 (tp)
REVERT: B  306 HIS cc_start: 0.9572 (OUTLIER) cc_final: 0.9298 (t-90)
  outliers start: 33
  outliers final: 20
  residues processed: 82
  average time/residue: 0.0845
  time to fit residues: 10.1355
Evaluate side-chains
  78 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 52
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 LEU
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue  102 GLN
Chi-restraints excluded: chain A residue  124 SER
Chi-restraints excluded: chain A residue  135 LYS
Chi-restraints excluded: chain A residue  243 HIS
Chi-restraints excluded: chain A residue  273 HIS
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  338 PHE
Chi-restraints excluded: chain A residue  410 SER
Chi-restraints excluded: chain A residue  411 GLN
Chi-restraints excluded: chain B residue   16 TYR
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   26 MET
Chi-restraints excluded: chain B residue   40 ILE
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  195 CYS
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  224 ILE
Chi-restraints excluded: chain B residue  249 ASP
Chi-restraints excluded: chain B residue  306 HIS
Chi-restraints excluded: chain B residue  328 ASP
Chi-restraints excluded: chain B residue  407 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 45 optimal weight:    4.9990
   chunk 17 optimal weight:    3.9990
   chunk 7 optimal weight:    3.9990
   chunk 5 optimal weight:    7.9990
   chunk 8 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9990
   chunk 27 optimal weight:    6.9990
   chunk 66 optimal weight:    8.9990
   chunk 81 optimal weight:   10.0000
   overall best weight:    1.7988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  80 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.070228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.052745 restraints weight = 51661.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.054473 restraints weight = 24843.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.055541 restraints weight = 16558.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.056058 restraints weight = 13231.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.056441 restraints weight = 11861.671|
|-----------------------------------------------------------------------------|
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.3197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   9766  Z= 0.164
  Angle     :  0.630  13.235  13891  Z= 0.341
  Chirality :  0.038   0.363   1619
  Planarity :  0.004   0.047   1207
  Dihedral  : 24.602 171.030   3079
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 14.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 27.29 %
    Favored  : 67.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.14 (0.31), residues: 736
  helix:  1.77 (0.26), residues: 360
  sheet: -1.05 (0.45), residues: 128
  loop : -1.81 (0.40), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 301 
 TYR   0.013   0.001   TYR A 210 
 PHE   0.023   0.001   PHE A 394 
 TRP   0.009   0.001   TRP A  51 
 HIS   0.005   0.001   HIS B 306 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00334 /  0.16 ( 9762)
  covalent geometry    : angle       0.61511 /  0.34 (13885)
  hydrogen bonds       : bond        0.05472 /  3.50 (  415)
  hydrogen bonds       : angle       3.80981 /  2.77 ( 1109)
  metal coordination   : bond        0.01066 /  0.50 (    4)
  metal coordination   : angle       6.65790 /  2.84 (    6)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 51
  time to evaluate  : 0.166 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8576 (mp)
REVERT: A  267 MET cc_start: 0.8921 (tpp) cc_final: 0.8615 (mmm)
REVERT: A  371 ARG cc_start: 0.8872 (tpm170) cc_final: 0.8321 (tpt90)
REVERT: A  372 HIS cc_start: 0.8706 (OUTLIER) cc_final: 0.8492 (t-90)
REVERT: B   16 TYR cc_start: 0.7967 (OUTLIER) cc_final: 0.7046 (p90)
REVERT: B   26 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8125 (mpp)
REVERT: B  206 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.7927 (tp)
REVERT: B  225 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7285 (mp)
REVERT: B  306 HIS cc_start: 0.9549 (OUTLIER) cc_final: 0.9336 (t-90)
  outliers start: 32
  outliers final: 21
  residues processed: 80
  average time/residue: 0.0747
  time to fit residues: 8.7943
Evaluate side-chains
  79 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 51
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 LEU
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue  102 GLN
Chi-restraints excluded: chain A residue  124 SER
Chi-restraints excluded: chain A residue  135 LYS
Chi-restraints excluded: chain A residue  273 HIS
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  338 PHE
Chi-restraints excluded: chain A residue  372 HIS
Chi-restraints excluded: chain A residue  389 THR
Chi-restraints excluded: chain A residue  410 SER
Chi-restraints excluded: chain A residue  411 GLN
Chi-restraints excluded: chain B residue   16 TYR
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   26 MET
Chi-restraints excluded: chain B residue   40 ILE
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  195 CYS
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  224 ILE
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  306 HIS
Chi-restraints excluded: chain B residue  328 ASP
Chi-restraints excluded: chain B residue  407 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 62 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 24 optimal weight:    0.6980
   chunk 8 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 85 optimal weight:   10.0000
   chunk 47 optimal weight:   10.0000
   chunk 22 optimal weight:    4.9990
   chunk 28 optimal weight:    0.7980
   overall best weight:    1.6984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  46 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.070151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.053453 restraints weight = 52383.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.054692 restraints weight = 26680.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.055145 restraints weight = 17434.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.055369 restraints weight = 16359.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.055326 restraints weight = 14862.787|
|-----------------------------------------------------------------------------|
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8206
moved from start:          0.3339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   9766  Z= 0.163
  Angle     :  0.632  12.808  13891  Z= 0.341
  Chirality :  0.038   0.345   1619
  Planarity :  0.004   0.049   1207
  Dihedral  : 24.524 171.130   3079
  Min Nonbonded Distance : 2.342

Molprobity Statistics.
  All-atom Clashscore : 14.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 26.51 %
    Favored  : 68.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.24 (0.32), residues: 736
  helix:  1.85 (0.26), residues: 360
  sheet: -0.98 (0.45), residues: 128
  loop : -1.77 (0.40), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 179 
 TYR   0.011   0.001   TYR A 348 
 PHE   0.010   0.001   PHE A  49 
 TRP   0.012   0.001   TRP A  51 
 HIS   0.005   0.001   HIS B 306 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00331 /  0.16 ( 9762)
  covalent geometry    : angle       0.61772 /  0.34 (13885)
  hydrogen bonds       : bond        0.05354 /  3.40 (  415)
  hydrogen bonds       : angle       3.79301 /  2.75 ( 1109)
  metal coordination   : bond        0.01034 /  0.48 (    4)
  metal coordination   : angle       6.35163 /  2.71 (    6)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 51
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8493 (mp)
REVERT: A  267 MET cc_start: 0.8929 (tpp) cc_final: 0.8564 (mmm)
REVERT: A  302 ASP cc_start: 0.9040 (OUTLIER) cc_final: 0.8592 (t0)
REVERT: A  371 ARG cc_start: 0.8969 (tpm170) cc_final: 0.8411 (tpt90)
REVERT: A  410 SER cc_start: 0.9422 (OUTLIER) cc_final: 0.8775 (t)
REVERT: B   16 TYR cc_start: 0.8032 (OUTLIER) cc_final: 0.7104 (p90)
REVERT: B   26 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8114 (mpp)
REVERT: B  206 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.7928 (tp)
REVERT: B  306 HIS cc_start: 0.9541 (OUTLIER) cc_final: 0.9315 (t-90)
  outliers start: 33
  outliers final: 17
  residues processed: 81
  average time/residue: 0.0880
  time to fit residues: 10.3138
Evaluate side-chains
  74 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 50
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 LEU
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue  102 GLN
Chi-restraints excluded: chain A residue  124 SER
Chi-restraints excluded: chain A residue  273 HIS
Chi-restraints excluded: chain A residue  302 ASP
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  338 PHE
Chi-restraints excluded: chain A residue  389 THR
Chi-restraints excluded: chain A residue  410 SER
Chi-restraints excluded: chain A residue  411 GLN
Chi-restraints excluded: chain B residue   16 TYR
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   26 MET
Chi-restraints excluded: chain B residue   40 ILE
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  306 HIS
Chi-restraints excluded: chain B residue  328 ASP
Chi-restraints excluded: chain B residue  407 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 35 optimal weight:    0.8980
   chunk 30 optimal weight:    0.8980
   chunk 71 optimal weight:    2.9990
   chunk 56 optimal weight:   20.0000
   chunk 75 optimal weight:   10.0000
   chunk 7 optimal weight:    5.9990
   chunk 25 optimal weight:    4.9990
   chunk 19 optimal weight:    0.0970
   chunk 79 optimal weight:   10.0000
   chunk 72 optimal weight:    0.0370
   chunk 73 optimal weight:    5.9990
   overall best weight:    0.9858

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  46 GLN
B  80 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.071059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.053652 restraints weight = 51434.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.055363 restraints weight = 24839.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.056408 restraints weight = 16585.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.057070 restraints weight = 13306.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.057322 restraints weight = 11704.205|
|-----------------------------------------------------------------------------|
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start:          0.3377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9766  Z= 0.131
  Angle     :  0.612  12.764  13891  Z= 0.330
  Chirality :  0.037   0.356   1619
  Planarity :  0.004   0.051   1207
  Dihedral  : 24.489 174.205   3079
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 12.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 27.60 %
    Favored  : 68.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.34 (0.32), residues: 736
  helix:  1.95 (0.26), residues: 360
  sheet: -0.83 (0.46), residues: 125
  loop : -1.82 (0.40), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 179 
 TYR   0.011   0.001   TYR B 308 
 PHE   0.013   0.001   PHE A 394 
 TRP   0.009   0.001   TRP A  51 
 HIS   0.005   0.001   HIS B 306 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00263 /  0.13 ( 9762)
  covalent geometry    : angle       0.59940 /  0.33 (13885)
  hydrogen bonds       : bond        0.05199 /  3.27 (  415)
  hydrogen bonds       : angle       3.65371 /  2.65 ( 1109)
  metal coordination   : bond        0.01282 /  0.61 (    4)
  metal coordination   : angle       6.02065 /  2.51 (    6)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 50
  time to evaluate  : 0.208 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8505 (mp)
REVERT: A   17 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7634 (mp)
REVERT: A  267 MET cc_start: 0.8934 (tpp) cc_final: 0.8588 (mmm)
REVERT: A  371 ARG cc_start: 0.8846 (tpm170) cc_final: 0.8319 (tpt90)
REVERT: A  410 SER cc_start: 0.9390 (OUTLIER) cc_final: 0.8651 (t)
REVERT: B   16 TYR cc_start: 0.7993 (OUTLIER) cc_final: 0.7065 (p90)
REVERT: B   26 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8068 (mpp)
REVERT: B  206 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.7933 (tp)
REVERT: B  306 HIS cc_start: 0.9523 (OUTLIER) cc_final: 0.9310 (t-90)
REVERT: B  312 LEU cc_start: 0.9616 (tp) cc_final: 0.9353 (pp)
REVERT: B  326 MET cc_start: 0.8461 (tmm) cc_final: 0.8092 (tmm)
  outliers start: 25
  outliers final: 15
  residues processed: 73
  average time/residue: 0.0800
  time to fit residues: 8.5587
Evaluate side-chains
  71 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 49
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 LEU
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue  102 GLN
Chi-restraints excluded: chain A residue  124 SER
Chi-restraints excluded: chain A residue  210 TYR
Chi-restraints excluded: chain A residue  273 HIS
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  338 PHE
Chi-restraints excluded: chain A residue  389 THR
Chi-restraints excluded: chain A residue  410 SER
Chi-restraints excluded: chain A residue  411 GLN
Chi-restraints excluded: chain B residue   16 TYR
Chi-restraints excluded: chain B residue   26 MET
Chi-restraints excluded: chain B residue   40 ILE
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  306 HIS
Chi-restraints excluded: chain B residue  328 ASP
Chi-restraints excluded: chain B residue  407 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 61 optimal weight:   20.0000
   chunk 32 optimal weight:    3.9990
   chunk 41 optimal weight:    3.9990
   chunk 38 optimal weight:    0.8980
   chunk 82 optimal weight:   10.0000
   chunk 6 optimal weight:    0.9980
   chunk 12 optimal weight:    0.0970
   chunk 9 optimal weight:    0.9980
   chunk 58 optimal weight:   10.0000
   chunk 31 optimal weight:    7.9990
   chunk 83 optimal weight:   10.0000
   overall best weight:    1.3980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  46 GLN
B  80 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.070854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.053407 restraints weight = 51646.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.055140 restraints weight = 24560.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.056216 restraints weight = 16278.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.056830 restraints weight = 12965.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.057182 restraints weight = 11458.874|
|-----------------------------------------------------------------------------|
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8136
moved from start:          0.3467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   9766  Z= 0.148
  Angle     :  0.617  13.171  13891  Z= 0.332
  Chirality :  0.038   0.436   1619
  Planarity :  0.004   0.053   1207
  Dihedral  : 24.463 173.040   3079
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 13.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 27.91 %
    Favored  : 68.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.41 (0.32), residues: 736
  helix:  1.96 (0.26), residues: 360
  sheet: -0.59 (0.45), residues: 131
  loop : -1.85 (0.40), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 179 
 TYR   0.017   0.001   TYR B 308 
 PHE   0.011   0.001   PHE A 394 
 TRP   0.010   0.001   TRP A  51 
 HIS   0.006   0.001   HIS B  80 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00306 /  0.15 ( 9762)
  covalent geometry    : angle       0.60306 /  0.33 (13885)
  hydrogen bonds       : bond        0.05161 /  3.25 (  415)
  hydrogen bonds       : angle       3.66462 /  2.66 ( 1109)
  metal coordination   : bond        0.01103 /  0.50 (    4)
  metal coordination   : angle       6.22408 /  2.58 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1541.82 seconds
wall clock time: 27 minutes 27.19 seconds (1647.19 seconds total)